I have a Windows 2008 server using the MS iSCSI initiator to connect to our Equallogic SAN. About 50% of the time when I reboot the server the shares on the iSCSI target disappear. The data and folders are there, just not the share. The shares on the local disks are fine.
I think the randomness of whether the shares disappear or not might be if they happen to be in use at the time of reboot, but I'm not 100% sure.